SAMBA-ilum 1.0.0.545__tar.gz → 1.0.0.546__tar.gz

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.545
+Version: 1.0.0.546
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.545
+Version: 1.0.0.546
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.545'
+version = '1.0.0.546'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/samba_ilum/src/cell_check.py

@@ -226,7 +226,7 @@ for name in files0:
                     #--------------------------------------------------------------
                     deslocamento_frac = np.array([-p_direto[0], -p_direto[1], 0.0])
                     print(f"Direct coordinates of the appropriate axis of rotation: ({p_direto[0]:.9f}, {p_direto[1]:.9f})")
-                    print(f"Moving original file to 'POSCAR_original' folder and creating corrected version.")
+                    print(f"Fixed POSCAR file")
                     #------------------------------------
                     estrutura_corrigida = estrutura.copy()
                     indices_dos_sites = list(range(len(estrutura_corrigida)))
@@ -248,85 +248,7 @@ for name in files0:
         print(f"Critical Error processing file {name}: {e}")
         if (axis_correction > 0): sys.exit()
 
+#------------------------
+shutil.rmtree(backup_dir)
 delete_hidden_files(poscar_dir_path)
-
-
-
-#============================================
-# creating IDs for POSCAR files =============
-#============================================
-id_poscar_files = open(dir_files + '/ID_POSCAR_Files.txt', 'w')
-for i in range(len(files0)):
-    #--------------------------------------------
-    Lattice0 = dir_files + '/' + dir_poscar + '/'
-    poscar = open(Lattice0 + files0[i], 'r')
-    VTemp1 = poscar.readline().split()
-    for j in range(4): VTemp = poscar.readline()
-    VTemp2 = poscar.readline().split()
-    VTemp3 = poscar.readline().split()
-    poscar.close()
-    #-------------
-    temp_ion = ''
-    temp_nion = 0
-    for j in range(len(VTemp2)):
-        temp_ion += str(VTemp2[j]) 
-        temp_nion += int(VTemp3[j])
-        if (j < (len(VTemp2) -1)): temp_ion += '_' 
-    #---------------------------------------------
-    if (VTemp1[0] != 'SAMBA'):
-       #----------------------
-       id_material = ''
-       #---------------------------------------
-       poscar = open(Lattice0 + files0[i], "r")
-       for j in range(5): VTemp = poscar.readline()
-       VTemp3 = poscar.readline().split()
-       VTemp4 = poscar.readline().split()
-       poscar.close()
-       #--------------------------------------------------------------------------------------------
-       # Creating a unique 16-digit ID that encodes the POSCAR file structure ----------------------
-       #--------------------------------------------------------------------------------------------
-       with open(Lattice0 + files0[i], 'r') as f: lines = [line.strip() for line in f.readlines() if line.strip()]
-       #----------------------
-       tag_1 = float(lines[1])
-       #---------
-       tag_2 = []
-       for j in range(2, 5):
-           vector = [float(x) for x in lines[j].split()]
-           tag_2.append(vector)
-       #-----------------------
-       tag_3 = lines[5].split()
-       #-----------------------
-       tag_4 = [int(x) for x in lines[6].split()]
-       #-----------------------------------------
-       tag_5 = lines[7].lower()
-       #-----------------------
-       tag_6 = []
-       natoms = sum(tag_4)
-       for j in range(8, 8 + natoms):
-           coord = [float(x) for x in lines[j].split()[:3]]
-           tag_6.append(coord)
-       #----------------------
-       data_hash = [tag_1, tag_2, tag_3, tag_4, tag_5, tag_6]
-       canonical_string = json.dumps(data_hash, separators=(',', ':'))
-       unique_id = hashlib.sha256(canonical_string.encode('utf-8')).hexdigest()[:16]
-       #----------------------------------------------------------------------------
-       for j in range(len(VTemp3)):
-           id_material += str(VTemp3[j])
-           if (str(VTemp4[j]) != '1'): id_material += str(VTemp4[j])
-       id_material +=  '_' + unique_id
-       #--------------------------------------------------------------------
-       with open(Lattice0 + files0[i], 'r') as file: line = file.readlines()
-       line[0] = 'SAMBA ' + temp_ion + ' ' + str(temp_nion) + ' ' + id_material + '\n'
-       with open(Lattice0 + files0[i], 'w') as file: file.writelines(line)
-       #------------------------------------------------------------------
-       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
-    #-------------------------
-    if (VTemp1[0] == 'SAMBA'):
-       #----------------------------
-       id_material = str(VTemp1[-1])
-       #--------------------------------------------------------
-       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
-#----------------------
-id_poscar_files.close()
-#----------------------
-
+#-----------------------------------

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/samba_ilum/src/poscar_fix_direct_coord.py

@@ -110,9 +110,86 @@ for file_in in files1:
        #-----------------------------------------------------------
        poscar_in.close()   
        poscar_out.close()
-       #-----------------
-
-#====================================
+#------------------------------------
 shutil.rmtree(poscar_backup_dir_path)
 delete_hidden_files(poscar_dir_path)
-#===================================
+#-----------------------------------
+
+
+#============================================
+# creating IDs for POSCAR files =============
+#============================================
+id_poscar_files = open(dir_files + '/ID_POSCAR_Files.txt', 'w')
+for i in range(len(files0)):
+    #--------------------------------------------
+    Lattice0 = dir_files + '/' + dir_poscar + '/'
+    poscar = open(Lattice0 + files0[i], 'r')
+    VTemp1 = poscar.readline().split()
+    for j in range(4): VTemp = poscar.readline()
+    VTemp2 = poscar.readline().split()
+    VTemp3 = poscar.readline().split()
+    poscar.close()
+    #-------------
+    temp_ion = ''
+    temp_nion = 0
+    for j in range(len(VTemp2)):
+        temp_ion += str(VTemp2[j]) 
+        temp_nion += int(VTemp3[j])
+        if (j < (len(VTemp2) -1)): temp_ion += '_' 
+    #---------------------------------------------
+    if (VTemp1[0] != 'SAMBA'):
+       #----------------------
+       id_material = ''
+       #---------------------------------------
+       poscar = open(Lattice0 + files0[i], "r")
+       for j in range(5): VTemp = poscar.readline()
+       VTemp3 = poscar.readline().split()
+       VTemp4 = poscar.readline().split()
+       poscar.close()
+       #--------------------------------------------------------------------------------------------
+       # Creating a unique 16-digit ID that encodes the POSCAR file structure ----------------------
+       #--------------------------------------------------------------------------------------------
+       with open(Lattice0 + files0[i], 'r') as f: lines = [line.strip() for line in f.readlines() if line.strip()]
+       #----------------------
+       tag_1 = float(lines[1])
+       #---------
+       tag_2 = []
+       for j in range(2, 5):
+           vector = [float(x) for x in lines[j].split()]
+           tag_2.append(vector)
+       #-----------------------
+       tag_3 = lines[5].split()
+       #-----------------------
+       tag_4 = [int(x) for x in lines[6].split()]
+       #-----------------------------------------
+       tag_5 = lines[7].lower()
+       #-----------------------
+       tag_6 = []
+       natoms = sum(tag_4)
+       for j in range(8, 8 + natoms):
+           coord = [float(x) for x in lines[j].split()[:3]]
+           tag_6.append(coord)
+       #----------------------
+       data_hash = [tag_1, tag_2, tag_3, tag_4, tag_5, tag_6]
+       canonical_string = json.dumps(data_hash, separators=(',', ':'))
+       unique_id = hashlib.sha256(canonical_string.encode('utf-8')).hexdigest()[:16]
+       #----------------------------------------------------------------------------
+       for j in range(len(VTemp3)):
+           id_material += str(VTemp3[j])
+           if (str(VTemp4[j]) != '1'): id_material += str(VTemp4[j])
+       id_material +=  '_' + unique_id
+       #--------------------------------------------------------------------
+       with open(Lattice0 + files0[i], 'r') as file: line = file.readlines()
+       line[0] = 'SAMBA ' + temp_ion + ' ' + str(temp_nion) + ' ' + id_material + '\n'
+       with open(Lattice0 + files0[i], 'w') as file: file.writelines(line)
+       #------------------------------------------------------------------
+       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
+    #-------------------------
+    if (VTemp1[0] == 'SAMBA'):
+       #----------------------------
+       id_material = str(VTemp1[-1])
+       #--------------------------------------------------------
+       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
+#----------------------
+id_poscar_files.close()
+#----------------------

{samba_ilum-1.0.0.545 → samba_ilum-1.0.0.546}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.545",
+    version = "1.0.0.546",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",